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Items: 1 to 50 of 203

1.

The structure of the bacterial iron-catecholate transporter Fiu suggests that it imports substrates via a two-step mechanism.

Grinter R, Lithgow T.

J Biol Chem. 2019 Nov 11. pii: jbc.RA119.011018. doi: 10.1074/jbc.RA119.011018. [Epub ahead of print]

2.

The multifunctional enzyme S-adenosylhomocysteine/methylthioadenosine nucleosidase is a key metabolic enzyme in the virulence of Salmonella enterica var Typhimurium.

Husna AU, Wang N, Wilksch JJ, Newton HJ, Hocking DM, Hay ID, Cobbold SA, Davies MR, McConville MJ, Lithgow T, Strugnell RA.

Biochem J. 2019 Nov 29;476(22):3435-3453. doi: 10.1042/BCJ20190297.

PMID:
31675053
3.

Protease-associated import systems are widespread in Gram-negative bacteria.

Grinter R, Leung PM, Wijeyewickrema LC, Littler D, Beckham S, Pike RN, Walker D, Greening C, Lithgow T.

PLoS Genet. 2019 Oct 15;15(10):e1008435. doi: 10.1371/journal.pgen.1008435. eCollection 2019 Oct.

4.

Structure of the mitochondrial import gate reveals distinct preprotein paths.

Araiso Y, Tsutsumi A, Qiu J, Imai K, Shiota T, Song J, Lindau C, Wenz LS, Sakaue H, Yunoki K, Kawano S, Suzuki J, Wischnewski M, Schütze C, Ariyama H, Ando T, Becker T, Lithgow T, Wiedemann N, Pfanner N, Kikkawa M, Endo T.

Nature. 2019 Nov;575(7782):395-401. doi: 10.1038/s41586-019-1680-7. Epub 2019 Oct 10.

PMID:
31600774
5.

The flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi-like protein tail fibre.

Dunstan RA, Pickard D, Dougan S, Goulding D, Cormie C, Hardy J, Li F, Grinter R, Harcourt K, Yu L, Song J, Schreiber F, Choudhary J, Clare S, Coulibaly F, Strugnell RA, Dougan G, Lithgow T.

Mol Microbiol. 2019 Sep 25. doi: 10.1111/mmi.14396. [Epub ahead of print]

PMID:
31556164
6.

An Outbreak of Carbapenem-Resistant and Hypervirulent Klebsiella pneumoniae in an Intensive Care Unit of a Major Teaching Hospital in Wenzhou, China.

Zhao Y, Zhang X, Torres VVL, Liu H, Rocker A, Zhang Y, Wang J, Chen L, Bi W, Lin J, Strugnell RA, Zhang S, Lithgow T, Zhou T, Cao J.

Front Public Health. 2019 Aug 19;7:229. doi: 10.3389/fpubh.2019.00229. eCollection 2019.

7.

Costs Attributable to Arteriovenous Fistula and Arteriovenous Graft Placements in Hemodialysis Patients with Medicare coverage.

Nordyke RJ, Reichert H, Bylsma LC, Jackson JJ, Gage SM, Fryzek J, Roy-Chaudhury P, Lithgow T.

Am J Nephrol. 2019;50(4):320-328. doi: 10.1159/000502507. Epub 2019 Aug 21.

PMID:
31434095
8.

PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins.

Zhang Y, Yu S, Xie R, Li J, Leier A, Marquez-Lago TT, Akutsu T, Smith AI, Ge Z, Wang J, Lithgow T, Song J.

Bioinformatics. 2019 Aug 8. pii: btz629. doi: 10.1093/bioinformatics/btz629. [Epub ahead of print]

PMID:
31393553
9.

Author Correction: Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics.

Davies MR, McIntyre L, Mutreja A, Lacey JA, Lees JA, Towers RJ, Duchêne S, Smeesters PR, Frost HR, Price DJ, Holden MTG, David S, Giffard PM, Worthing KA, Seale AC, Berkley JA, Harris SR, Rivera-Hernandez T, Berking O, Cork AJ, Torres RSLA, Lithgow T, Strugnell RA, Bergmann R, Nitsche-Schmitz P, Chhatwal GS, Bentley SD, Fraser JD, Moreland NJ, Carapetis JR, Steer AC, Parkhill J, Saul A, Williamson DA, Currie BJ, Tong SYC, Dougan G, Walker MJ.

Nat Genet. 2019 Aug;51(8):1295. doi: 10.1038/s41588-019-0482-z.

PMID:
31324894
10.

Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics.

Davies MR, McIntyre L, Mutreja A, Lacey JA, Lees JA, Towers RJ, Duchêne S, Smeesters PR, Frost HR, Price DJ, Holden MTG, David S, Giffard PM, Worthing KA, Seale AC, Berkley JA, Harris SR, Rivera-Hernandez T, Berking O, Cork AJ, Torres RSLA, Lithgow T, Strugnell RA, Bergmann R, Nitsche-Schmitz P, Chhatwal GS, Bentley SD, Fraser JD, Moreland NJ, Carapetis JR, Steer AC, Parkhill J, Saul A, Williamson DA, Currie BJ, Tong SYC, Dougan G, Walker MJ.

Nat Genet. 2019 Jun;51(6):1035-1043. doi: 10.1038/s41588-019-0417-8. Epub 2019 May 27. Erratum in: Nat Genet. 2019 Jul 19;:.

11.

Determination of the molecular basis for coprogen import by Gram-negative bacteria.

Grinter R, Lithgow T.

IUCrJ. 2019 Apr 5;6(Pt 3):401-411. doi: 10.1107/S2052252519002926. eCollection 2019 May 1.

12.

Filamentous phages: masters of a microbial sharing economy.

Hay ID, Lithgow T.

EMBO Rep. 2019 Jun;20(6). pii: e47427. doi: 10.15252/embr.201847427. Epub 2019 Apr 5. Review.

PMID:
30952693
13.

Positive-unlabelled learning of glycosylation sites in the human proteome.

Li F, Zhang Y, Purcell AW, Webb GI, Chou KC, Lithgow T, Li C, Song J.

BMC Bioinformatics. 2019 Mar 6;20(1):112. doi: 10.1186/s12859-019-2700-1.

14.

The TAM: A Translocation and Assembly Module of the β-Barrel Assembly Machinery in Bacterial Outer Membranes.

Stubenrauch CJ, Lithgow T.

EcoSal Plus. 2019 Feb;8(2). doi: 10.1128/ecosalplus.ESP-0036-2018. Review.

PMID:
30816086
15.

Porin Associates with Tom22 to Regulate the Mitochondrial Protein Gate Assembly.

Sakaue H, Shiota T, Ishizaka N, Kawano S, Tamura Y, Tan KS, Imai K, Motono C, Hirokawa T, Taki K, Miyata N, Kuge O, Lithgow T, Endo T.

Mol Cell. 2019 Mar 7;73(5):1044-1055.e8. doi: 10.1016/j.molcel.2019.01.003. Epub 2019 Feb 6.

PMID:
30738703
16.

Clinical Outcomes of Arteriovenous Access in Incident Hemodialysis Patients with Medicare Coverage, 2012-2014.

Bylsma LC, Reichert H, Gage SM, Roy-Chaudhury P, Nordyke RJ, Fryzek J, Dahl SLM, Lithgow T, Lawson JH.

Am J Nephrol. 2019;49(2):156-164. doi: 10.1159/000495355. Epub 2019 Jan 24.

PMID:
30677763
17.

cryoEM-Guided Development of Antibiotics for Drug-Resistant Bacteria.

Belousoff MJ, Venugopal H, Wright A, Seoner S, Stuart I, Stubenrauch C, Bamert RS, Lupton DW, Lithgow T.

ChemMedChem. 2019 Mar 5;14(5):527-531. doi: 10.1002/cmdc.201900042. Epub 2019 Feb 12.

PMID:
30667174
18.

Bastion3: a two-layer ensemble predictor of type III secreted effectors.

Wang J, Li J, Yang B, Xie R, Marquez-Lago TT, Leier A, Hayashida M, Akutsu T, Zhang Y, Chou KC, Selkrig J, Zhou T, Song J, Lithgow T.

Bioinformatics. 2019 Jun 1;35(12):2017-2028. doi: 10.1093/bioinformatics/bty914.

PMID:
30388198
19.

Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods.

Li F, Wang Y, Li C, Marquez-Lago TT, Leier A, Rawlings ND, Haffari G, Revote J, Akutsu T, Chou KC, Purcell AW, Pike RN, Webb GI, Ian Smith A, Lithgow T, Daly RJ, Whisstock JC, Song J.

Brief Bioinform. 2018 Aug 29. doi: 10.1093/bib/bby077. [Epub ahead of print]

PMID:
30184176
20.

FusC, a member of the M16 protease family acquired by bacteria for iron piracy against plants.

Grinter R, Hay ID, Song J, Wang J, Teng D, Dhanesakaran V, Wilksch JJ, Davies MR, Littler D, Beckham SA, Henderson IR, Strugnell RA, Dougan G, Lithgow T.

PLoS Biol. 2018 Aug 2;16(8):e2006026. doi: 10.1371/journal.pbio.2006026. eCollection 2018 Aug.

21.

Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.

Li F, Li C, Marquez-Lago TT, Leier A, Akutsu T, Purcell AW, Ian Smith A, Lithgow T, Daly RJ, Song J, Chou KC.

Bioinformatics. 2018 Dec 15;34(24):4223-4231. doi: 10.1093/bioinformatics/bty522.

PMID:
29947803
22.

An investigation into the Omp85 protein BamK in hypervirulent Klebsiella pneumoniae, and its role in outer membrane biogenesis.

Torres VVL, Heinz E, Stubenrauch CJ, Wilksch JJ, Cao H, Yang J, Clements A, Dunstan RA, Alcock F, Webb CT, Dougan G, Strugnell RA, Hay ID, Lithgow T.

Mol Microbiol. 2018 Sep;109(5):584-599. doi: 10.1111/mmi.13990. Epub 2018 Sep 19.

PMID:
29873128
23.

The WD40 Protein BamB Mediates Coupling of BAM Complexes into Assembly Precincts in the Bacterial Outer Membrane.

Gunasinghe SD, Shiota T, Stubenrauch CJ, Schulze KE, Webb CT, Fulcher AJ, Dunstan RA, Hay ID, Naderer T, Whelan DR, Bell TDM, Elgass KD, Strugnell RA, Lithgow T.

Cell Rep. 2018 May 29;23(9):2782-2794. doi: 10.1016/j.celrep.2018.04.093.

24.

Methionine biosynthesis and transport are functionally redundant for the growth and virulence of Salmonella Typhimurium.

Husna AU, Wang N, Cobbold SA, Newton HJ, Hocking DM, Wilksch JJ, Scott TA, Davies MR, Hinton JC, Tree JJ, Lithgow T, McConville MJ, Strugnell RA.

J Biol Chem. 2018 Jun 15;293(24):9506-9519. doi: 10.1074/jbc.RA118.002592. Epub 2018 May 2.

25.

Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa.

Zhu Y, Czauderna T, Zhao J, Klapperstueck M, Maifiah MHM, Han ML, Lu J, Sommer B, Velkov T, Lithgow T, Song J, Schreiber F, Li J.

Gigascience. 2018 Apr 1;7(4). doi: 10.1093/gigascience/giy021.

26.

Outer membrane vesicles from Neisseria gonorrhoeae target PorB to mitochondria and induce apoptosis.

Deo P, Chow SH, Hay ID, Kleifeld O, Costin A, Elgass KD, Jiang JH, Ramm G, Gabriel K, Dougan G, Lithgow T, Heinz E, Naderer T.

PLoS Pathog. 2018 Mar 30;14(3):e1006945. doi: 10.1371/journal.ppat.1006945. eCollection 2018 Mar.

27.

Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors.

Wang J, Yang B, Leier A, Marquez-Lago TT, Hayashida M, Rocker A, Zhang Y, Akutsu T, Chou KC, Strugnell RA, Song J, Lithgow T.

Bioinformatics. 2018 Aug 1;34(15):2546-2555. doi: 10.1093/bioinformatics/bty155.

28.

Correction for Nguyen et al., "Bacteriophage Transcytosis Provides a Mechanism To Cross Epithelial Cell Layers".

Nguyen S, Baker K, Padman BS, Patwa R, Dunstan RA, Weston TA, Schlosser K, Bailey B, Lithgow T, Lazarou M, Luque A, Rohwer F, Blumberg RS, Barr JJ.

MBio. 2018 Jan 2;9(1). pii: e02207-17. doi: 10.1128/mBio.02207-17. No abstract available.

29.

Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches.

Wang J, Yang B, An Y, Marquez-Lago T, Leier A, Wilksch J, Hong Q, Zhang Y, Hayashida M, Akutsu T, Webb GI, Strugnell RA, Song J, Lithgow T.

Brief Bioinform. 2019 May 21;20(3):931-951. doi: 10.1093/bib/bbx164.

30.

Bacteriophage Transcytosis Provides a Mechanism To Cross Epithelial Cell Layers.

Nguyen S, Baker K, Padman BS, Patwa R, Dunstan RA, Weston TA, Schlosser K, Bailey B, Lithgow T, Lazarou M, Luque A, Rohwer F, Blumberg RS, Barr JJ.

MBio. 2017 Nov 21;8(6). pii: e01874-17. doi: 10.1128/mBio.01874-17. Erratum in: MBio. 2018 Jan 2;9(1):.

31.

Constraints on lateral gene transfer in promoting fimbrial usher protein diversity and function.

Stubenrauch CJ, Dougan G, Lithgow T, Heinz E.

Open Biol. 2017 Nov;7(11). pii: 170144. doi: 10.1098/rsob.170144.

32.

The Structure of a Conserved Domain of TamB Reveals a Hydrophobic β Taco Fold.

Josts I, Stubenrauch CJ, Vadlamani G, Mosbahi K, Walker D, Lithgow T, Grinter R.

Structure. 2017 Dec 5;25(12):1898-1906.e5. doi: 10.1016/j.str.2017.10.002. Epub 2017 Nov 9.

33.

Structure and Membrane Topography of the Vibrio-Type Secretin Complex from the Type 2 Secretion System of Enteropathogenic Escherichia coli.

Hay ID, Belousoff MJ, Dunstan RA, Bamert RS, Lithgow T.

J Bacteriol. 2018 Feb 7;200(5). pii: e00521-17. doi: 10.1128/JB.00521-17. Print 2018 Mar 1.

34.

Reductive evolution in outer membrane protein biogenesis has not compromised cell surface complexity in Helicobacter pylori.

Webb CT, Chandrapala D, Oslan SN, Bamert RS, Grinter RD, Dunstan RA, Gorrell RJ, Song J, Strugnell RA, Lithgow T, Kwok T.

Microbiologyopen. 2017 Dec;6(6). doi: 10.1002/mbo3.513. Epub 2017 Oct 21.

35.

Phylogenetic Analysis of Klebsiella pneumoniae from Hospitalized Children, Pakistan.

Ejaz H, Wang N, Wilksch JJ, Page AJ, Cao H, Gujaran S, Keane JA, Lithgow T, Ul-Haq I, Dougan G, Strugnell RA, Heinz E.

Emerg Infect Dis. 2017 Nov;23(11):1872-1875. doi: 10.3201/eid2311.170833.

36.

Structural Basis of Type 2 Secretion System Engagement between the Inner and Outer Bacterial Membranes.

Hay ID, Belousoff MJ, Lithgow T.

MBio. 2017 Oct 17;8(5). pii: e01344-17. doi: 10.1128/mBio.01344-17.

37.

The TPR domain of BepA is required for productive interaction with substrate proteins and the β-barrel assembly machinery complex.

Daimon Y, Iwama-Masui C, Tanaka Y, Shiota T, Suzuki T, Miyazaki R, Sakurada H, Lithgow T, Dohmae N, Mori H, Tsukazaki T, Narita SI, Akiyama Y.

Mol Microbiol. 2017 Dec;106(5):760-776. doi: 10.1111/mmi.13844. Epub 2017 Oct 17.

38.

POSSUM: a bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles.

Wang J, Yang B, Revote J, Leier A, Marquez-Lago TT, Webb G, Song J, Chou KC, Lithgow T.

Bioinformatics. 2017 Sep 1;33(17):2756-2758. doi: 10.1093/bioinformatics/btx302.

PMID:
28903538
39.

Structural basis for substrate selection by the translocation and assembly module of the β-barrel assembly machinery.

Bamert RS, Lundquist K, Hwang H, Webb CT, Shiota T, Stubenrauch CJ, Belousoff MJ, Goode RJA, Schittenhelm RB, Zimmerman R, Jung M, Gumbart JC, Lithgow T.

Mol Microbiol. 2017 Oct;106(1):142-156. doi: 10.1111/mmi.13757. Epub 2017 Aug 9.

40.

Knowledge-transfer learning for prediction of matrix metalloprotease substrate-cleavage sites.

Wang Y, Song J, Marquez-Lago TT, Leier A, Li C, Lithgow T, Webb GI, Shen HB.

Sci Rep. 2017 Jul 18;7(1):5755. doi: 10.1038/s41598-017-06219-7.

41.

Extensively Drug-Resistant Klebsiella pneumoniae Causing Nosocomial Bloodstream Infections in China: Molecular Investigation of Antibiotic Resistance Determinants, Informing Therapy, and Clinical Outcomes.

Bi W, Liu H, Dunstan RA, Li B, Torres VVL, Cao J, Chen L, Wilksch JJ, Strugnell RA, Lithgow T, Zhou T.

Front Microbiol. 2017 Jun 30;8:1230. doi: 10.3389/fmicb.2017.01230. eCollection 2017.

42.

Defining Membrane Protein Localization by Isopycnic Density Gradients.

Dunstan RA, Hay ID, Lithgow T.

Methods Mol Biol. 2017;1615:81-86. doi: 10.1007/978-1-4939-7033-9_6.

PMID:
28667604
43.

Super-Resolution Imaging of Protein Secretion Systems and the Cell Surface of Gram-Negative Bacteria.

Gunasinghe SD, Webb CT, Elgass KD, Hay ID, Lithgow T.

Front Cell Infect Microbiol. 2017 May 29;7:220. doi: 10.3389/fcimb.2017.00220. eCollection 2017. Review.

44.

Structural Basis for Linezolid Binding Site Rearrangement in the Staphylococcus aureus Ribosome.

Belousoff MJ, Eyal Z, Radjainia M, Ahmed T, Bamert RS, Matzov D, Bashan A, Zimmerman E, Mishra S, Cameron D, Elmlund H, Peleg AY, Bhushan S, Lithgow T, Yonath A.

MBio. 2017 May 9;8(3). pii: e00395-17. doi: 10.1128/mBio.00395-17.

45.

SecretEPDB: a comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems.

An Y, Wang J, Li C, Revote J, Zhang Y, Naderer T, Hayashida M, Akutsu T, Webb GI, Lithgow T, Song J.

Sci Rep. 2017 Jan 23;7:41031. doi: 10.1038/srep41031.

46.

Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI.

An Y, Wang J, Li C, Leier A, Marquez-Lago T, Wilksch J, Zhang Y, Webb GI, Song J, Lithgow T.

Brief Bioinform. 2018 Jan 1;19(1):148-161. doi: 10.1093/bib/bbw100.

PMID:
27777222
47.

GlycoMinestruct: a new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features.

Li F, Li C, Revote J, Zhang Y, Webb GI, Li J, Song J, Lithgow T.

Sci Rep. 2016 Oct 6;6:34595. doi: 10.1038/srep34595.

48.

The modular nature of the β-barrel assembly machinery, illustrated in Borrelia burgdorferi.

Stubenrauch C, Grinter R, Lithgow T.

Mol Microbiol. 2016 Dec;102(5):753-756. doi: 10.1111/mmi.13527. Epub 2016 Sep 30.

49.

Effective assembly of fimbriae in Escherichia coli depends on the translocation assembly module nanomachine.

Stubenrauch C, Belousoff MJ, Hay ID, Shen HH, Lillington J, Tuck KL, Peters KM, Phan MD, Lo AW, Schembri MA, Strugnell RA, Waksman G, Lithgow T.

Nat Microbiol. 2016 May 16;1(7):16064. doi: 10.1038/nmicrobiol.2016.64.

PMID:
27572967
50.

Eliminating Legionella by inhibiting BCL-XL to induce macrophage apoptosis.

Speir M, Lawlor KE, Glaser SP, Abraham G, Chow S, Vogrin A, Schulze KE, Schuelein R, O'Reilly LA, Mason K, Hartland EL, Lithgow T, Strasser A, Lessene G, Huang DC, Vince JE, Naderer T.

Nat Microbiol. 2016 Feb 24;1:15034. doi: 10.1038/nmicrobiol.2015.34.

PMID:
27572165

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